Software | Name | Classification |
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CNS | refinementDENZO | data reductionSCALEPACK | data scalingCNS | phasing | | | |
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Refinement | Method to determine structure: MAD / Resolution: 1.85→28.78 Å / Rfactor Rfree error: 0.005 / Data cutoff high absF: 2704063.75 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber
| Rfactor | Num. reflection | % reflection | Selection details |
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Rfree | 0.242 | 2895 | 5.8 % | RANDOM |
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Rwork | 0.22 | - | - | - |
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all | - | 49714 | - | - |
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obs | - | 49714 | 99.7 % | - |
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Solvent computation | Solvent model: FLAT MODEL / Bsol: 39.8378 Å2 / ksol: 0.354021 e/Å3 |
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Displacement parameters | Biso mean: 31.3 Å2
| Baniso -1 | Baniso -2 | Baniso -3 |
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1- | -8.11 Å2 | 0 Å2 | 0 Å2 |
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2- | - | 17.64 Å2 | 0 Å2 |
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3- | - | - | -9.54 Å2 |
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Refine analyze | | Free | Obs |
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Luzzati coordinate error | 0.27 Å | 0.23 Å |
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Luzzati d res low | - | 5 Å |
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Luzzati sigma a | 0.17 Å | 0.13 Å |
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Refinement step | Cycle: LAST / Resolution: 1.85→28.78 Å
| Protein | Nucleic acid | Ligand | Solvent | Total |
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Num. atoms | 4086 | 0 | 20 | 212 | 4318 |
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Refine LS restraints | Refine-ID | Type | Dev ideal |
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X-RAY DIFFRACTION | c_bond_d0.01 | X-RAY DIFFRACTION | c_angle_deg1.5 | X-RAY DIFFRACTION | c_dihedral_angle_d23.4 | X-RAY DIFFRACTION | c_improper_angle_d0.9 | | | | |
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LS refinement shell | Resolution: 1.85→1.97 Å / Rfactor Rfree error: 0.014 / Total num. of bins used: 6
| Rfactor | Num. reflection | % reflection |
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Rfree | 0.282 | 421 | 5.1 % |
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Rwork | 0.24 | 7755 | - |
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obs | - | - | 99.9 % |
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Xplor file | Refine-ID | Serial no | Param file | Topol file |
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X-RAY DIFFRACTION | 1 | PROTEIN_REP.PARAMPROTEIN.TOPX-RAY DIFFRACTION | 2 | WATER_REP.PARAMWATER.TOPX-RAY DIFFRACTION | 3 | ION.PARAMION.TOP | | | | | |
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Software | *PLUS Name: CNS / Version: 1 / Classification: refinement |
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Refinement | *PLUS Num. reflection obs: 46819 / σ(F): 0 / % reflection Rfree: 5.8 % / Rfactor obs: 0.22 / Rfactor Rwork: 0.22 |
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Solvent computation | *PLUS |
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Displacement parameters | *PLUS Biso mean: 31.3 Å2 |
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Refine LS restraints | *PLUS Refine-ID | Type | Dev ideal |
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X-RAY DIFFRACTION | c_angle_deg1.5 | X-RAY DIFFRACTION | c_dihedral_angle_d | X-RAY DIFFRACTION | c_dihedral_angle_deg23.4 | X-RAY DIFFRACTION | c_improper_angle_d | X-RAY DIFFRACTION | c_improper_angle_deg0.9 | | | | | |
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LS refinement shell | *PLUS Rfactor Rfree: 0.282 / % reflection Rfree: 5.1 % / Rfactor Rwork: 0.24 / Rfactor obs: 0.24 |
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